Calcium in PDB 6q8g: Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution
Protein crystallography data
The structure of Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution, PDB code: 6q8g
was solved by
S.Baeriswyl,
A.Stocker,
J.-L.Reymond,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.92 /
1.19
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
56.445,
72.085,
123.593,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
14.5 /
16.1
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution
(pdb code 6q8g). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the
Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution, PDB code: 6q8g:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Calcium binding site 1 out
of 8 in 6q8g
Go back to
Calcium Binding Sites List in 6q8g
Calcium binding site 1 out
of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca301
b:13.1
occ:1.00
|
OD1
|
A:ASP99
|
2.4
|
17.8
|
1.0
|
OD1
|
A:ASP101
|
2.4
|
13.4
|
1.0
|
OE2
|
A:GLU95
|
2.4
|
14.2
|
1.0
|
OD2
|
A:ASP104
|
2.4
|
12.4
|
1.0
|
OE1
|
A:GLU95
|
2.5
|
13.7
|
1.0
|
O3
|
E:ZDC1
|
2.5
|
14.3
|
1.0
|
O4
|
E:ZDC1
|
2.5
|
14.2
|
1.0
|
OD1
|
A:ASP104
|
2.6
|
12.2
|
1.0
|
CD
|
A:GLU95
|
2.7
|
13.9
|
1.0
|
CG
|
A:ASP104
|
2.9
|
11.8
|
1.0
|
C4
|
E:ZDC1
|
3.3
|
14.4
|
1.0
|
C3
|
E:ZDC1
|
3.4
|
14.4
|
1.0
|
CG
|
A:ASP99
|
3.4
|
17.3
|
1.0
|
CG
|
A:ASP101
|
3.4
|
14.1
|
1.0
|
OD2
|
A:ASP99
|
3.7
|
17.0
|
1.0
|
CA
|
A:CA302
|
3.7
|
12.4
|
1.0
|
OD2
|
A:ASP101
|
3.9
|
14.3
|
1.0
|
O
|
A:HOH463
|
4.1
|
20.8
|
1.0
|
N
|
A:ASP101
|
4.1
|
15.9
|
1.0
|
CG
|
A:GLU95
|
4.2
|
13.7
|
1.0
|
OD1
|
A:ASP96
|
4.3
|
13.8
|
1.0
|
CB
|
A:ASP104
|
4.4
|
11.3
|
1.0
|
N
|
A:TYR102
|
4.4
|
12.8
|
1.0
|
N
|
A:ASN100
|
4.5
|
16.1
|
1.0
|
N
|
A:ASP96
|
4.5
|
12.7
|
1.0
|
CB
|
A:ASP101
|
4.6
|
16.1
|
1.0
|
N
|
A:GLY97
|
4.6
|
13.6
|
1.0
|
CA
|
A:GLU95
|
4.7
|
11.5
|
1.0
|
C2
|
E:ZDC1
|
4.7
|
15.2
|
1.0
|
C5
|
E:ZDC1
|
4.7
|
15.3
|
1.0
|
CA
|
A:ASP101
|
4.7
|
14.4
|
1.0
|
CB
|
A:ASP99
|
4.7
|
18.1
|
1.0
|
OD1
|
A:ASN103
|
4.7
|
11.8
|
1.0
|
N
|
A:ASP99
|
4.8
|
17.0
|
1.0
|
O2
|
E:ZDC1
|
4.8
|
14.6
|
1.0
|
CB
|
A:GLU95
|
4.9
|
12.8
|
1.0
|
C
|
A:ASP101
|
5.0
|
13.5
|
1.0
|
C
|
A:ASP99
|
5.0
|
17.4
|
1.0
|
CG
|
A:ASP96
|
5.0
|
12.2
|
1.0
|
|
Calcium binding site 2 out
of 8 in 6q8g
Go back to
Calcium Binding Sites List in 6q8g
Calcium binding site 2 out
of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca302
b:12.4
occ:1.00
|
OD1
|
A:ASN103
|
2.3
|
11.8
|
1.0
|
O
|
A:ASN21
|
2.4
|
13.2
|
1.0
|
OD1
|
A:ASP104
|
2.4
|
12.2
|
1.0
|
OD2
|
A:ASP101
|
2.4
|
14.3
|
1.0
|
O
|
B:GLY114
|
2.4
|
14.3
|
1.0
|
O2
|
E:ZDC1
|
2.5
|
14.6
|
1.0
|
O3
|
E:ZDC1
|
2.5
|
14.3
|
1.0
|
OD1
|
A:ASP101
|
3.1
|
13.4
|
1.0
|
CG
|
A:ASP101
|
3.1
|
14.1
|
1.0
|
C3
|
E:ZDC1
|
3.4
|
14.4
|
1.0
|
CG
|
A:ASN103
|
3.4
|
11.0
|
1.0
|
C
|
B:GLY114
|
3.4
|
14.9
|
1.0
|
C2
|
E:ZDC1
|
3.4
|
15.2
|
1.0
|
C
|
A:ASN21
|
3.6
|
11.7
|
1.0
|
CG
|
A:ASP104
|
3.6
|
11.8
|
1.0
|
OXT
|
B:GLY114
|
3.6
|
17.7
|
1.0
|
CA
|
A:CA301
|
3.7
|
13.1
|
1.0
|
C4
|
E:ZDC1
|
3.8
|
14.4
|
1.0
|
ND2
|
A:ASN103
|
3.8
|
13.3
|
1.0
|
CB
|
A:ASN21
|
4.1
|
11.8
|
1.0
|
CA
|
A:ASP104
|
4.2
|
10.4
|
1.0
|
N
|
A:ASP104
|
4.3
|
11.3
|
1.0
|
CA
|
A:SER22
|
4.4
|
13.5
|
1.0
|
N
|
A:SER22
|
4.4
|
12.5
|
1.0
|
O4
|
E:ZDC1
|
4.5
|
14.2
|
1.0
|
OD2
|
A:ASP104
|
4.5
|
12.4
|
1.0
|
C
|
A:ASN103
|
4.5
|
10.8
|
1.0
|
CB
|
A:ASP104
|
4.5
|
11.3
|
1.0
|
CA
|
A:ASN21
|
4.5
|
11.7
|
1.0
|
OD2
|
A:ASP99
|
4.5
|
17.0
|
1.0
|
O
|
A:HOH456
|
4.5
|
25.7
|
1.0
|
CB
|
A:ASP101
|
4.6
|
16.1
|
1.0
|
CB
|
A:SER22
|
4.7
|
12.3
|
1.0
|
CB
|
A:ASN103
|
4.7
|
11.6
|
1.0
|
C1
|
E:ZDC1
|
4.8
|
15.8
|
1.0
|
CA
|
B:GLY114
|
4.8
|
15.2
|
1.0
|
O
|
A:ASN103
|
4.8
|
11.1
|
1.0
|
N
|
A:ASN103
|
4.9
|
11.4
|
1.0
|
CA
|
A:ASN103
|
4.9
|
11.6
|
1.0
|
O5
|
E:ZDC1
|
5.0
|
14.5
|
1.0
|
|
Calcium binding site 3 out
of 8 in 6q8g
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Calcium Binding Sites List in 6q8g
Calcium binding site 3 out
of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca303
b:10.8
occ:1.00
|
OD1
|
B:ASN103
|
2.3
|
10.2
|
1.0
|
OD1
|
B:ASP104
|
2.3
|
11.2
|
1.0
|
O
|
B:ASN21
|
2.4
|
11.2
|
1.0
|
OD2
|
B:ASP101
|
2.4
|
11.8
|
1.0
|
O
|
A:GLY114
|
2.4
|
11.9
|
1.0
|
O2
|
F:ZDC1
|
2.5
|
12.3
|
1.0
|
O3
|
F:ZDC1
|
2.5
|
12.1
|
1.0
|
OD1
|
B:ASP101
|
3.0
|
11.5
|
1.0
|
CG
|
B:ASP101
|
3.1
|
12.0
|
1.0
|
CG
|
B:ASN103
|
3.4
|
9.6
|
1.0
|
C3
|
F:ZDC1
|
3.4
|
12.4
|
1.0
|
C
|
A:GLY114
|
3.4
|
12.4
|
1.0
|
C2
|
F:ZDC1
|
3.4
|
12.7
|
1.0
|
C
|
B:ASN21
|
3.6
|
11.0
|
1.0
|
CG
|
B:ASP104
|
3.6
|
10.6
|
1.0
|
OXT
|
A:GLY114
|
3.6
|
13.9
|
1.0
|
CA
|
B:CA301
|
3.7
|
11.2
|
1.0
|
ND2
|
B:ASN103
|
3.7
|
11.6
|
1.0
|
C4
|
F:ZDC1
|
3.8
|
12.8
|
1.0
|
CB
|
B:ASN21
|
4.1
|
10.3
|
1.0
|
CA
|
B:ASP104
|
4.2
|
10.2
|
1.0
|
N
|
B:ASP104
|
4.3
|
10.0
|
1.0
|
CA
|
B:SER22
|
4.4
|
12.3
|
1.0
|
N
|
B:SER22
|
4.4
|
11.6
|
1.0
|
OD2
|
B:ASP104
|
4.4
|
11.1
|
1.0
|
O4
|
F:ZDC1
|
4.4
|
12.7
|
1.0
|
CB
|
B:ASP104
|
4.5
|
10.2
|
1.0
|
O
|
B:HOH454
|
4.5
|
23.0
|
1.0
|
OD2
|
B:ASP99
|
4.5
|
14.7
|
1.0
|
C
|
B:ASN103
|
4.5
|
10.3
|
1.0
|
CA
|
B:ASN21
|
4.5
|
10.6
|
1.0
|
CB
|
B:ASP101
|
4.5
|
13.4
|
1.0
|
CB
|
B:SER22
|
4.6
|
11.7
|
1.0
|
CB
|
B:ASN103
|
4.7
|
10.4
|
1.0
|
CA
|
A:GLY114
|
4.8
|
12.5
|
1.0
|
C1
|
F:ZDC1
|
4.8
|
13.7
|
1.0
|
O
|
B:ASN103
|
4.8
|
10.2
|
1.0
|
N
|
B:ASN103
|
4.9
|
9.8
|
1.0
|
CA
|
B:ASN103
|
5.0
|
9.9
|
1.0
|
OD1
|
B:ASP99
|
5.0
|
15.6
|
1.0
|
|
Calcium binding site 4 out
of 8 in 6q8g
Go back to
Calcium Binding Sites List in 6q8g
Calcium binding site 4 out
of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca301
b:11.2
occ:1.00
|
OD1
|
B:ASP99
|
2.4
|
15.6
|
1.0
|
OD1
|
B:ASP101
|
2.4
|
11.5
|
1.0
|
OD2
|
B:ASP104
|
2.4
|
11.1
|
1.0
|
OE2
|
B:GLU95
|
2.4
|
11.8
|
1.0
|
OE1
|
B:GLU95
|
2.5
|
11.3
|
1.0
|
O3
|
F:ZDC1
|
2.5
|
12.1
|
1.0
|
O4
|
F:ZDC1
|
2.5
|
12.7
|
1.0
|
OD1
|
B:ASP104
|
2.6
|
11.2
|
1.0
|
CD
|
B:GLU95
|
2.8
|
11.3
|
1.0
|
CG
|
B:ASP104
|
2.9
|
10.6
|
1.0
|
C4
|
F:ZDC1
|
3.3
|
12.8
|
1.0
|
CG
|
B:ASP99
|
3.4
|
15.7
|
1.0
|
C3
|
F:ZDC1
|
3.4
|
12.4
|
1.0
|
CG
|
B:ASP101
|
3.4
|
12.0
|
1.0
|
OD2
|
B:ASP99
|
3.7
|
14.7
|
1.0
|
CA
|
A:CA303
|
3.7
|
10.8
|
1.0
|
OD2
|
B:ASP101
|
3.9
|
11.8
|
1.0
|
O
|
B:HOH460
|
4.1
|
22.0
|
1.0
|
N
|
B:ASP101
|
4.2
|
13.2
|
1.0
|
OD1
|
B:ASP96
|
4.3
|
13.7
|
1.0
|
CG
|
B:GLU95
|
4.3
|
12.0
|
1.0
|
CB
|
B:ASP104
|
4.4
|
10.2
|
1.0
|
N
|
B:TYR102
|
4.5
|
10.7
|
1.0
|
N
|
B:ASP96
|
4.5
|
11.5
|
1.0
|
N
|
B:ASN100
|
4.5
|
14.3
|
1.0
|
N
|
B:GLY97
|
4.6
|
13.1
|
1.0
|
CB
|
B:ASP101
|
4.6
|
13.4
|
1.0
|
OD1
|
B:ASN103
|
4.7
|
10.2
|
1.0
|
CA
|
B:GLU95
|
4.7
|
9.9
|
1.0
|
C2
|
F:ZDC1
|
4.7
|
12.7
|
1.0
|
CB
|
B:ASP99
|
4.7
|
15.0
|
1.0
|
C5
|
F:ZDC1
|
4.7
|
14.7
|
1.0
|
CA
|
B:ASP101
|
4.8
|
12.1
|
1.0
|
N
|
B:ASP99
|
4.8
|
15.0
|
1.0
|
O2
|
F:ZDC1
|
4.8
|
12.3
|
1.0
|
CB
|
B:GLU95
|
4.9
|
11.4
|
1.0
|
CG
|
B:ASP96
|
5.0
|
12.1
|
1.0
|
CA
|
B:GLY97
|
5.0
|
15.1
|
1.0
|
|
Calcium binding site 5 out
of 8 in 6q8g
Go back to
Calcium Binding Sites List in 6q8g
Calcium binding site 5 out
of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca301
b:13.7
occ:1.00
|
OD1
|
C:ASP99
|
2.3
|
17.8
|
1.0
|
OD1
|
C:ASP101
|
2.3
|
14.9
|
1.0
|
OE2
|
C:GLU95
|
2.4
|
14.7
|
1.0
|
OD2
|
C:ASP104
|
2.4
|
13.6
|
1.0
|
OE1
|
C:GLU95
|
2.4
|
13.9
|
1.0
|
O3
|
G:ZDC1
|
2.5
|
14.1
|
1.0
|
O4
|
G:ZDC1
|
2.5
|
14.9
|
1.0
|
OD1
|
C:ASP104
|
2.6
|
13.7
|
1.0
|
CD
|
C:GLU95
|
2.7
|
13.7
|
1.0
|
CG
|
C:ASP104
|
2.9
|
13.5
|
1.0
|
C4
|
G:ZDC1
|
3.3
|
15.2
|
1.0
|
CG
|
C:ASP99
|
3.4
|
17.7
|
1.0
|
C3
|
G:ZDC1
|
3.4
|
14.6
|
1.0
|
CG
|
C:ASP101
|
3.4
|
14.3
|
1.0
|
OD2
|
C:ASP99
|
3.7
|
16.6
|
1.0
|
CA
|
C:CA302
|
3.7
|
13.6
|
1.0
|
OD2
|
C:ASP101
|
4.0
|
14.3
|
1.0
|
O
|
C:HOH477
|
4.1
|
22.1
|
1.0
|
N
|
C:ASP101
|
4.1
|
15.9
|
1.0
|
OD1
|
C:ASP96
|
4.2
|
16.6
|
1.0
|
CG
|
C:GLU95
|
4.2
|
14.2
|
1.0
|
CB
|
C:ASP104
|
4.4
|
14.7
|
1.0
|
N
|
C:TYR102
|
4.5
|
13.0
|
1.0
|
N
|
C:ASN100
|
4.5
|
16.7
|
1.0
|
N
|
C:ASP96
|
4.5
|
13.1
|
1.0
|
CB
|
C:ASP101
|
4.6
|
14.8
|
1.0
|
N
|
C:GLY97
|
4.6
|
14.9
|
1.0
|
CA
|
C:GLU95
|
4.7
|
13.1
|
1.0
|
CB
|
C:ASP99
|
4.7
|
17.9
|
1.0
|
C2
|
G:ZDC1
|
4.7
|
14.3
|
1.0
|
CA
|
C:ASP101
|
4.7
|
14.8
|
1.0
|
C5
|
G:ZDC1
|
4.7
|
17.3
|
1.0
|
OD1
|
C:ASN103
|
4.8
|
13.5
|
1.0
|
N
|
C:ASP99
|
4.8
|
17.2
|
1.0
|
O2
|
G:ZDC1
|
4.8
|
14.8
|
1.0
|
CB
|
C:GLU95
|
4.9
|
12.5
|
1.0
|
C
|
C:ASP99
|
4.9
|
17.3
|
1.0
|
CG
|
C:ASP96
|
4.9
|
15.4
|
1.0
|
C
|
C:ASP101
|
5.0
|
13.4
|
1.0
|
|
Calcium binding site 6 out
of 8 in 6q8g
Go back to
Calcium Binding Sites List in 6q8g
Calcium binding site 6 out
of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca302
b:13.6
occ:1.00
|
O
|
C:ASN21
|
2.3
|
15.1
|
1.0
|
OD1
|
C:ASN103
|
2.3
|
13.5
|
1.0
|
OD1
|
C:ASP104
|
2.4
|
13.7
|
1.0
|
OD2
|
C:ASP101
|
2.4
|
14.3
|
1.0
|
O
|
D:GLY114
|
2.4
|
14.9
|
1.0
|
O2
|
G:ZDC1
|
2.5
|
14.8
|
1.0
|
O3
|
G:ZDC1
|
2.5
|
14.1
|
1.0
|
CG
|
C:ASP101
|
3.1
|
14.3
|
1.0
|
OD1
|
C:ASP101
|
3.1
|
14.9
|
1.0
|
CG
|
C:ASN103
|
3.4
|
13.1
|
1.0
|
C3
|
G:ZDC1
|
3.4
|
14.6
|
1.0
|
C
|
D:GLY114
|
3.4
|
17.4
|
1.0
|
C2
|
G:ZDC1
|
3.4
|
14.3
|
1.0
|
C
|
C:ASN21
|
3.5
|
14.9
|
1.0
|
CG
|
C:ASP104
|
3.6
|
13.5
|
1.0
|
OXT
|
D:GLY114
|
3.6
|
19.3
|
1.0
|
CA
|
C:CA301
|
3.7
|
13.7
|
1.0
|
ND2
|
C:ASN103
|
3.8
|
13.6
|
1.0
|
C4
|
G:ZDC1
|
3.8
|
15.2
|
1.0
|
CB
|
C:ASN21
|
4.1
|
13.8
|
1.0
|
CA
|
C:ASP104
|
4.2
|
13.0
|
1.0
|
N
|
C:ASP104
|
4.3
|
12.2
|
1.0
|
CA
|
C:SER22
|
4.4
|
15.9
|
1.0
|
N
|
C:SER22
|
4.4
|
15.2
|
1.0
|
O4
|
G:ZDC1
|
4.5
|
14.9
|
1.0
|
OD2
|
C:ASP104
|
4.5
|
13.6
|
1.0
|
C
|
C:ASN103
|
4.5
|
12.9
|
1.0
|
O
|
C:HOH436
|
4.5
|
24.5
|
1.0
|
CB
|
C:ASP104
|
4.5
|
14.7
|
1.0
|
CA
|
C:ASN21
|
4.5
|
14.4
|
1.0
|
CB
|
C:ASP101
|
4.5
|
14.8
|
1.0
|
OD2
|
C:ASP99
|
4.5
|
16.6
|
1.0
|
CB
|
C:SER22
|
4.6
|
16.9
|
1.0
|
CB
|
C:ASN103
|
4.7
|
12.9
|
1.0
|
C1
|
G:ZDC1
|
4.8
|
16.1
|
1.0
|
CA
|
D:GLY114
|
4.8
|
17.1
|
1.0
|
O
|
C:ASN103
|
4.8
|
13.2
|
1.0
|
N
|
C:ASN103
|
4.9
|
11.8
|
1.0
|
CA
|
C:ASN103
|
4.9
|
13.3
|
1.0
|
O5
|
G:ZDC1
|
5.0
|
15.7
|
1.0
|
|
Calcium binding site 7 out
of 8 in 6q8g
Go back to
Calcium Binding Sites List in 6q8g
Calcium binding site 7 out
of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca304
b:15.7
occ:1.00
|
O
|
D:ASN21
|
2.3
|
17.2
|
1.0
|
OD1
|
D:ASN103
|
2.3
|
15.4
|
1.0
|
OD1
|
D:ASP104
|
2.4
|
16.4
|
1.0
|
OD2
|
D:ASP101
|
2.4
|
17.6
|
1.0
|
O2
|
C:ZDC303
|
2.4
|
17.2
|
1.0
|
O
|
C:GLY114
|
2.4
|
17.0
|
1.0
|
O3
|
C:ZDC303
|
2.5
|
17.8
|
1.0
|
OD1
|
D:ASP101
|
3.1
|
17.3
|
1.0
|
CG
|
D:ASP101
|
3.1
|
18.1
|
1.0
|
CG
|
D:ASN103
|
3.4
|
14.3
|
1.0
|
C3
|
C:ZDC303
|
3.4
|
18.2
|
1.0
|
C2
|
C:ZDC303
|
3.4
|
18.4
|
1.0
|
C
|
C:GLY114
|
3.4
|
18.5
|
1.0
|
C
|
D:ASN21
|
3.5
|
16.3
|
1.0
|
CG
|
D:ASP104
|
3.6
|
15.8
|
1.0
|
OXT
|
C:GLY114
|
3.6
|
20.5
|
1.0
|
CA
|
D:CA201
|
3.7
|
16.7
|
1.0
|
ND2
|
D:ASN103
|
3.8
|
15.9
|
1.0
|
C4
|
C:ZDC303
|
3.8
|
18.8
|
1.0
|
CB
|
D:ASN21
|
4.1
|
15.6
|
1.0
|
CA
|
D:ASP104
|
4.2
|
14.5
|
1.0
|
N
|
D:ASP104
|
4.3
|
14.0
|
1.0
|
CA
|
D:SER22
|
4.4
|
17.9
|
1.0
|
N
|
D:SER22
|
4.4
|
16.4
|
1.0
|
OD2
|
D:ASP104
|
4.4
|
16.2
|
1.0
|
O4
|
C:ZDC303
|
4.4
|
17.6
|
1.0
|
CB
|
D:ASP104
|
4.5
|
15.7
|
1.0
|
C
|
D:ASN103
|
4.5
|
14.7
|
1.0
|
CA
|
D:ASN21
|
4.5
|
15.8
|
1.0
|
OD2
|
D:ASP99
|
4.5
|
20.5
|
1.0
|
O
|
D:HOH358
|
4.5
|
28.4
|
1.0
|
CB
|
D:ASP101
|
4.5
|
18.9
|
1.0
|
CB
|
D:SER22
|
4.6
|
18.3
|
1.0
|
CB
|
D:ASN103
|
4.7
|
14.4
|
1.0
|
C1
|
C:ZDC303
|
4.8
|
19.0
|
1.0
|
CA
|
C:GLY114
|
4.8
|
16.8
|
1.0
|
O
|
D:ASN103
|
4.8
|
14.4
|
1.0
|
N
|
D:ASN103
|
4.9
|
14.0
|
1.0
|
CA
|
D:ASN103
|
4.9
|
13.9
|
1.0
|
OD1
|
D:ASP99
|
5.0
|
20.3
|
1.0
|
O5
|
C:ZDC303
|
5.0
|
19.3
|
1.0
|
|
Calcium binding site 8 out
of 8 in 6q8g
Go back to
Calcium Binding Sites List in 6q8g
Calcium binding site 8 out
of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Structure of Fucosylated D-Antimicrobial Peptide SB8 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.190 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca201
b:16.7
occ:1.00
|
OD1
|
D:ASP99
|
2.3
|
20.3
|
1.0
|
OD1
|
D:ASP101
|
2.4
|
17.3
|
1.0
|
OE1
|
D:GLU95
|
2.4
|
17.7
|
1.0
|
OD2
|
D:ASP104
|
2.4
|
16.2
|
1.0
|
O3
|
C:ZDC303
|
2.4
|
17.8
|
1.0
|
O4
|
C:ZDC303
|
2.5
|
17.6
|
1.0
|
OE2
|
D:GLU95
|
2.5
|
17.1
|
1.0
|
OD1
|
D:ASP104
|
2.6
|
16.4
|
1.0
|
CD
|
D:GLU95
|
2.8
|
18.2
|
1.0
|
CG
|
D:ASP104
|
2.9
|
15.8
|
1.0
|
C4
|
C:ZDC303
|
3.3
|
18.8
|
1.0
|
CG
|
D:ASP99
|
3.4
|
19.1
|
1.0
|
C3
|
C:ZDC303
|
3.4
|
18.2
|
1.0
|
CG
|
D:ASP101
|
3.4
|
18.1
|
1.0
|
OD2
|
D:ASP99
|
3.7
|
20.5
|
1.0
|
CA
|
C:CA304
|
3.7
|
15.7
|
1.0
|
OD2
|
D:ASP101
|
3.9
|
17.6
|
1.0
|
O
|
D:HOH368
|
4.0
|
25.3
|
1.0
|
N
|
D:ASP101
|
4.1
|
17.7
|
1.0
|
OD1
|
D:ASP96
|
4.2
|
19.1
|
1.0
|
CG
|
D:GLU95
|
4.3
|
18.1
|
1.0
|
CB
|
D:ASP104
|
4.4
|
15.7
|
1.0
|
N
|
D:TYR102
|
4.5
|
15.9
|
1.0
|
N
|
D:ASP96
|
4.5
|
15.7
|
1.0
|
N
|
D:ASN100
|
4.5
|
20.1
|
1.0
|
N
|
D:GLY97
|
4.6
|
17.9
|
1.0
|
CB
|
D:ASP101
|
4.6
|
18.9
|
1.0
|
CA
|
D:GLU95
|
4.7
|
14.3
|
1.0
|
C2
|
C:ZDC303
|
4.7
|
18.4
|
1.0
|
CB
|
D:ASP99
|
4.7
|
21.2
|
1.0
|
CA
|
D:ASP101
|
4.7
|
17.2
|
1.0
|
OD1
|
D:ASN103
|
4.7
|
15.4
|
1.0
|
C5
|
C:ZDC303
|
4.8
|
19.7
|
1.0
|
N
|
D:ASP99
|
4.8
|
20.0
|
1.0
|
O2
|
C:ZDC303
|
4.8
|
17.2
|
1.0
|
CB
|
D:GLU95
|
4.9
|
16.1
|
1.0
|
CG
|
D:ASP96
|
4.9
|
18.7
|
1.0
|
C
|
D:ASP99
|
5.0
|
20.0
|
1.0
|
C
|
D:ASP101
|
5.0
|
16.2
|
1.0
|
|
Reference:
S.Baeriswyl,
B.H.Gan,
T.N.Siriwardena,
R.Visini,
M.Robadey,
S.Javor,
A.Stocker,
T.Darbre,
J.L.Reymond.
X-Ray Crystal Structures of Short Antimicrobial Peptides As Pseudomonas Aeruginosa Lectin B Complexes. Acs Chem.Biol. V. 14 758 2019.
ISSN: ESSN 1554-8937
PubMed: 30830745
DOI: 10.1021/ACSCHEMBIO.9B00047
Page generated: Tue Jul 16 13:43:16 2024
|